[gmx-users] possible configuration for gromacs gpu node

[Szilárd Páll]

Indeed, sorry for the oversight, I read K5000 iso K4000. That should
be indeed fast enough for your system.

Btw, the 10-core 2.5 Ghz Xeon (2670?) will be a better
price/performance - for the same price - as the  E5-2643V2, at least
for GROMACS and in general codes that scale well.

--
Szilárd


On Wed, May 7, 2014 at 11:47 AM, Harry Mark Greenblatt
<harry.greenblatt at weizmann.ac.il> wrote:
> BS"D
>
> Dear Szilárd,
>
>   Thanks for your reply.
>
>
> Hence, to get a balanced hardware combination (assuming the same input
> system and settings), you would need a GPU that's about 2x faster than
> the K5000.
>
> Is that a typo?  We used a K4000, with half the number of CUDA cores (768) from what we are proposing (1536)
>
>
>
> * The GROMACS non-bonded kernels are compute-bound, so one can compare
> roughly performance of two cards of identical compute capability (!)
> by looking at the ratio of #multiprocessor*frequency (assuming an
> input large enough to reach the peak of the respective GPU), i.e. for
> K5000 vs GTX 770 roughly (1085*8)/(706.0*8)
>
> Not quite understanding the numbers:  the advertised GPU frequency for the 770 is 1085 MHz which appears above.  But the maximum clock speed of the K4000 card we have, based on the Nvidia configuration utility, is 549MHz, not 706.  And the value of "8" refers to the dedicated FP64 cores?  Then for the K4000 this is only 4, not 8, I believe.  So we should get a roughly (1085 x 8)/(549 x 4) = 3.9 fold improvement from the GTX 770 (in theory).
>
> Thanks
>
> Harry
>
>
>
>
> -------------------------------------------------------------------------
>
> Harry M. Greenblatt
>
> Associate Staff Scientist
>
> Dept of Structural Biology           Harry.Greenblatt at weizmann.ac.il<mailto:arry.Greenblatt at weizmann.ac.il>
>
> Weizmann Institute of Science        Phone:  972-8-934-3625
>
> 234 Herzl St.                        Facsimile:   972-8-934-4159
>
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>
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>
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